Vol 17, No 4 (2019)

Genetic basis of ecosystems evolution
Organization of the endoplasmic reticulum in cells of effective and ineffective pea nodules (Pisum sativum L.)
Tsyganova A.V., Tsyganov V.E.
Abstract

Background. The endoplasmic reticulum (ER) is the largest membrane-bound organelle, which plays an important role in the functioning of a plant cell and participates in its differentiation.

Materials and methods. Using the methods of transmission electron microscopy, the morphological features and dynamics of structural changes in the ER in symbiotic nodules of pea (Pisum sativum L.) wild-type and mutants blocked at different stages of nodule development were studied.

Results. ER developed from a network of individual tubules in meristematic cells, to a developed network of cisterns around the nucleus and plasmalemma, and a network of granular and smooth tubules accompanying infection structures in colonized and infected cells and symbiosomes in infected cells.

Conclusions. A correlation was found between the level of development of the ER network and the degree of bacteroid differentiation.

Ecological genetics. 2019;17(4):5-14
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The assessment of the genetic structure of bush snail (Fruticicola fruticum) populations based on the nonspecific esterases loci
Snegin E.A., Snegina E.A., Artemchuk O.Y.
Abstract

Using the polymorphic esterases loci, the genetic structure of the gastropod mollusk Fruticicola (Bradybaena) fruticum Мüll., most of which lives in the south of the Central Russian Upland, was studied. For comparison, the samples were taken from the Romania, the North Caucasus, the Ural and the Vyatka regions. A total of the 1668 individuals were investigated. Of the 28 studied populations in 11 (39.3%), there was significant shortage of the heterozygotes. The level of the expected heterozygosity fluctuated in the range He = 0.116–0.454. Using the non-parametric statistics (Chao1-bc method and 1st order jackknife method), the populations with potentially high and low diversity of the multilocus genotypes were identified. The indicators of the genetic disunity between populations averaged Φst = 0.276, Fst = 0.292. The principal component analysis and the Mantel correlation criterion Rм = –0.007 showed the absence of a reliable relationship between the geographical and genetic distance between populations, which indicates a violation of the isolation model by distance and confirms the thesis put forward by us that the urbanized forest-steppe landscape disrupts the natural migration processes, leads to the strong isolation and the genetic drift in the snail populations. At the same time, the phenomenon of increasing the degree of division of the populations against the background of reduced the allelic diversity, noted by us in many groups of bush snails, can be regarded as a shift in genetic equilibrium towards an increase in the interpopupulation diversity (according to the Wright model). The revealed absence of the effect of isolation by distance can be a consequence of the action of the stabilizing natural selection. The assumption of the dependence of the esterase alleles frequencies in the bush snail populations on the genetic (biochemical) characteristics of the food objects was proposed. The effective size, calculated using the Slatkin formula turned out to be comparable with the background, adventive and relict species of the terrestrial mollusks living in the study area (Ne = 2.2–7.6).

Ecological genetics. 2019;17(4):15-26
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The study of hybridization processes within genus Sparganium L. Subgenus Xanthosparganium holmb. Based on data of next generation sequencing (NGS)
Belyakov E.A., Machs E.M., Mikhailova Y.V., Rodionov A.V.
Abstract

The study represents the results of research of intragenic polymorphism in transcribed spacer ITS1 of the 35S rRNA genes in representatives of subgenus Xanthosparganium genus Sparganium which were obtained by means of locus-specific next generation sequencing on the platform Illumina MiSeq. It was shown that ribotype variations in studied samples generally correspond to the division of this genus into three sections – Erecta (subgenus Sparganium), Natantia and Minima (subgenus Xanthosparganium). High level of intragenic polymorphism was revealed in S. hyperboreum, with ribotypes distributed among several groups. Genome of this species includes ribotypes which are typical for other species in subgenus Xanthosparganium. For two investigated S. glomeratum samples, there were no ribotypes similar to such ribotypes in other species of Natantia section. S. glomeratum has got ribotypes identical with S. hyperboreum of Minima section. This feature may be the evidence of ancient intersectional hybridization of these two species. Characteristics of rDNA in S. glomeratum are in favor of putting this species into Minima section. It was suggested that speciation processes within the genus could be based not only on hybridization but also went on in allopatric way. The fist statement is supported by the presence of similar and identical ribotypes in S. emersum, S. × longifolium, S. gramineum and S. hyperboreum, the second – as it was mentioned by other researchers, is due to close relationship between North American and Eurasian taxa.

Ecological genetics. 2019;17(4):27-35
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Ecological genetics of Adalia beetles: variability and symbiotic bacteria in european populations of the ten-spot ladybird beetle Adalia decempunctata
Shaikevich E.V., Zakharov I.A., Honek A.
Abstract

Background. Adalia decempunctata L. (Coleoptera: Coccinellidae) — ten-spot ladybird beetle, widespread morphologically variable Palearctic species.

Materials and methods. DNA polymorphism and infection with Wolbachia, Spiroplasma and Rickettsia symbiotic bacteria were investigated.

Results. Eight different haplotypes of the mitochondrial COI gene, seven of which were previously unknown, were found in 92 A. decempunctata individuals from nine European collection places: Prague, Rome, Florence, Hamburg, Paris, Stockholm, Moscow, Feodosia and Yalta. A. decempunctata is less variable in mtDNA compared to A. bipunctata. Symbiotic bacteria Wolbachia and Spiroplasma were not detected. Only Rickettsia infestation was found in A. decempunctata specimens, gathered in Stockholm and Feodosia. Rickettsia from A. decempunctata from Feodosia and Stockholm differ by 0.5% in gltA gene. Rickettsia from A. decempunctata from Feodosia is clustered with Rickettsia from A. bipunctata and Coccinella sp. based on the analysis of the gltA gene.

Conclusion: Three of the eight mtDNA haplotypes are present in the A. decempunctata gene pool from geographically distant habitats. A small amount of nucleotide substitutions between Rickettsia from A. decempunctata and A. bipunctata suggests a single origin of the symbiont in the ladybirds of the genus Adalia, the results do not exclude subsequent horizontal transfers between individuals of both species.

Ecological genetics. 2019;17(4):37-45
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The analysis of the polyamine oxidase genes in the methylotrophic yeast Komagataella phaffii
Ivanova A.V., Sidorin A.V., Sambuk E.V., Rumyantsev A.M.
Abstract

Polyamines are present in all living cells and regulate a wide range of biological processes. In Saccharomyces cerevisiae the polyamine oxidase Fms1p converts spermine to spermidine and 3-aminopropionaldehyde, which is necessary for the synthesis of pantothenic acid and hypusination. This paper shows that S. cerevisiae FMS1 gene orthologs are present in all major representatives of the Saccharomycotina subdivision, but their copy numbers are different. In the Komagataella phaffii (Pichia pastoris) yeast, two polyamine oxidase genes (KpFMS1 and KpFMS2) were identified, and the regulation of their promoters activity was studied.

Ecological genetics. 2019;17(4):47-55
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Genetic toxicology
Micronuclei in blood lumphocytes of existing and former coal miners: evaluation of the effect of anthracosilicosis
Druzhinin V.G., Apalko S.V., Baranova E.D., Volobaev V.P., Drobchik T.Y., Larionov A.V., Hill E.G., Chasovskikh E.V.
Abstract

Background. The purpose of this study was to investigate the genotoxic risk in anthracosilicosis patients and in those with occupational exposure to coal dust.

Materials and methods. We studied micronuclei (MN) and other cytogenetic lesions in blood lymphocytes in three groups of men comparable in age: 74 coal miners suffering from anthracosilicosis (AS), 41 healthy miners, and 70 control donors.

Results. A significant increase in the frequency of MN was revealed with a simultaneous decrease in proliferative activity in samples of healthy and sick miners compared with the control. The level of MN in the lymphocytes of patients with AS significantly exceeded the corresponding indicator in the sample of healthy miners (1.22 ± 0.05% versus 1.03 ± 0.07%; p < 0.01). The age of the subjects and the status of smoking did not have a significant effect on the frequency of cytogenetic parameters.

Conclusion. AS in miners makes an additional contribution to the formation of DNA damage in lymphocytes. This contribution is probably due to oxidative stress accompanying inflammatory processes in pulmonary fibrosis. The results of the study also indicate the absence of differences in the frequency of MN when comparing subgroups of current and former miners. This means that the genotoxic effects in the lymphocytes of miners are able to persist for a long time after the termination of exposure by adverse factors in coal mining.

Ecological genetics. 2019;17(4):57-64
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Human ecological genetics
Genetic susceptibility to juvenile idiopathic arthritis in the Belarusian population: gene-gene interactions analysis
Yatskiu H.A., Savina N.V., Nikitchenko N.V., Kuzhir T.D., Tchitchko A.M., Sukalo A.V., Goncharova R.I.
Abstract

Background. GWASs revealed a huge amount of candidate genes for juvenile idiopathic arthritis (JIA) susceptibility. Individual SNP analysis has restrictions as an effect of each substitution may be too subtle to be detected but their interactions may significantly contribute to disease susceptibility.

Materials and methods. 118 patients diagnosed with JIA and 202 controls were included into the study. The study was aimed to estimate interactions between SNPs of the immune and inflammatory responses genes: RUNX3 (rs11249215), RUNX1 (rs9979383), STAT4 (rs7574865), TRAF1/C5 (rs3761847), MIF (rs755622), CTLA4 (rs5742909, rs231775), PTPN2 (rs2542151) and to reveal their effects on the JIA susceptibility. SNPs were genotyped using PCR-RFLP and Real-time PCR. Multifactor dimensionality reduction analysis was performed using MDR 3.0.2 software.

Results. RUNX3, STAT4 and PTPN2 polymorphisms were associated with systemic arthritis, RF- polyarthritis and oligoarthritis respectively. Interaction of CTLA4 (rs5742909, rs231775), TRAF1/C5 (rs3761847), RUNX1 (rs9979383), PTPN2 (rs2542151) SNPs is shown to be a risk factor for JIA (p = 0.0099).

Conclusion. Some of the SNPs studied are associated with distinct JIA subtypes. MDR analysis identified a statistically significant high-order interaction of five polymorphisms which collectively may contribute to JIA genetic susceptibility in the Belarusian population.

Ecological genetics. 2019;17(4):65-76
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The polygenic nature of rheumatoid arthritis
Kuzhir T.D.
Abstract

Current advances in the genetic basis of rheumatoid arthritis (RA) were summarized in the review. Influence of gene polymorphisms involved in different cellular processes including cytokine-mediated signal transduction, immune and inflammatory responses to exogenous stimuli was discussed. The principal role of the major histocompatibility complex (MHC) and a shared epitope (SE), as well as contribution of non-HLA genes to susceptibility to RA was considered in terms of patients’ ethnicity and the serological status for the disease. The GWAS results for revealing candidate genes closely associated with RA risk were systematized as well as some aspects of epigenetics were mentioned. The findings indicated the polygenic nature of this complex disease. This problem was considered taking into account the recent results of mapping traits (eQTLs) with global gene expression. The novel “omnigenic” conception of heritability of complex traits/diseases was reported.

Ecological genetics. 2019;17(4):77-90
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Effects of the intestinal microbiota on epigenetic mechanisms involved in the development of post-stress neuro-inflammation
Shalaginova I.G., Matskova L.V., Gunitseva N.M., Vakoliuk I.A.
Abstract

A number of alleles of polymorphic genes, dysfunctions of the hypothalamic-pituitary-adrenal axis, neurotransmitter disorders, and manifestations of immune dysregulation are associated with vulnerability to stress. Post-stress states of humans and animals are accompanied by signs of neuroinflammation, the causes and mechanisms of which remain to be elucidated. The article discusses epigenetic mechanisms by which the intestinal microbiota might participate in the initiation and maintenance of post-stress inflammation.

Ecological genetics. 2019;17(4):91-102
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Problems in genetic education
About stress, ... Or about Hans Selye’s two errors, conquered the world
Daev E.V.
Abstract

Too broad understanding of the term “stress”, which Selye himself and his followers used in their popular science works, reduces its scientific value. Based on a brief analysis of examples of the ambiguity of the term “stress”, it is proposed to restore its research significance. For that, the concept of “stress” should be used more strictly and unequivocally and it would not be allowed to use a “commonly broad” understanding the term in scientific papers. In the frame of earlier Selye’s stress definition, it suggests a more detailed structuring of the term based on levels of studying of living objects, including genetic.

Ecological genetics. 2019;17(4):103-111
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